Orientador: Maria Luiza Silveira Mello / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-07T20:32:58Z (GMT). No. of bitstreams: 1 Mampumbu_AndreRoberto_D.pdf: 659647 bytes, checksum: 40d0a48fa1d02750dffb30ae80b25445 (MD5) Previous issue date: 2006 / Resumo: O gênero Melipona (abelhas sem ferrão) tem sido dividido em dois grupos, com base no seu conteúdo em heterocromatina revelada com a técnica de banda-C em cromossomos mitóticos. Melipona quadrifasciata e Melipona rufiventris apresentam, respectivamente, níveis baixos e altos de heterocromatina. Na suposição de que cromatina condensada possa ser rica em seqüências de DNA metiladas, M. quadrifasciata e M. rufiventris poderiam então apresentar diferenças em conteúdo de seqüências CpG metiladas. Se isso acontecesse, as diferenças poderiam ser reveladas pela comparação de valores Feulgen-DNA obtidos por análise de imagem de células tratadas com as enzimas de restrição Msp I e Hpa II, que distinguem entre seqüências metiladas e não metiladas. Msp I e Hpa II clivam as seqüências ¿CCGG-, porém não há clivagem pela Hpa II se a citosina do dinucleotídeo central CG for metilada. Neste trabalho, túbulos de Malpighi de larva de último estádio de M. quadrifasciata e M. rufiventris submetidos à reação de Feulgen precedida pelo tratamento com Msp I e Hpa II tiveram suas células analisadas por microespectrofotometria de varredura automática. Para esse material houve necessidade do desenvolvimento prévio de um ajuste metodológico que tornasse a reação de Feulgen reveladora apenas de DNA, visto que ocorria reação plasmal; isto foi conseguido com um tratamento por boridreto de sódio a 5% e acetona/clorofórmio (1:1, v/v) antecedendo a reação de Feulgen. Também, embora a definição de altos e baixos conteúdos de heterocromatina em Melipona pela técnica de banda-C não fosse extensível à cromatina de núcleos interfásicos dos túbulos de Malpighi dessas abelhas, demonstrou-se que a depurinação do DNA em M. quadrifasciata era mais rápida do que a de M. rufiventris, confirmando, maiores teores de cromatina condensada em M. rufiventris. Os valores Feulgen-DNA para a heterocromatina de Melipona rufiventris e para a pouca heterocromatina somada a alguns domínios de eucromatina de Melipona quadrifasciata diminuíram após tratamento com Msp I, porém ficaram inalterados após tratamento com Hpa II. Conclui-se que seqüências CpG metiladas podem estar contidas em diferentes compartimentos cromatínicos, conforme a espécie do gênero Melipona considerada, e que os seus efeitos silenciadores possam atuar induzindo uma mesma fisiologia celular / Abstract: The genus Mellipona has been divided into two groups based on its heterochromatin content revealed by C-banding pattern in mitotic chromosomes. Melipona quadrifasciata and Melipona rufiventris show low and high heterochromatin content, respectively. Supposing that condensed chromatin may be rich in DNA methylated sequences, M quadrifasciata and M. rufiventris could, thus, show differences regarding their content of CpG methylated sequences. In this situation, such differences could be revealed by comparing the Feulgen-DNA values acquired after image analysis of cells treated with restriction enzymes Msp I and Hpa II, which distinguish between methylated and nonmethylated sequences. Msp I and Hpa II break the CCGG sequences. Nevertheless, Hpa II is ubable to break the DNA strand if the cytosine from the central nucleotide pair CG is methylated. In this work, Malpighian tubules from larvae from the last stage of M. quadrifasciata and M. rufiventris, subjected to the Feulgen reaction after by treatment with Msp I and Hpa II, were analysed in automatic scanning microspectrophotometry. Since a plasmal reaction was observed in this material, it was previously necessary the development of a methodological adjustement to make the Feulgen reaction specific to DNA. This was achieved by treatment of material with 5% sodium borohydrade followed by acetone-chloroform (1:1, v/v) before the Feulgen reaction. Also, although the definition of high and low heterochromatin content in Melipona after C-banding technique is not applicable to the chromatin of interphasic nuclei in Malpighian tubules of bees, it was demonstrated that DNA depurination in M. quadrifasciata was faster than that of M. rufiventris, thus confirming that this species has a higher condensed chromatin content. The Feulgen-DNA values for the heterochromatin of Melipona rufiventris, and for the heterochromatin besides some euchromatic domains of Melipona quadrifasciata, decreased after treatment with Msp I, remaining, however, unaltered after treatment with Hpa II. In conclusion, methylated CpG sequences may be part of different chromatin compartments, according to the considered species of the genus Melipona, and that their silencing effects may act by inducing the same cell physiology / Doutorado / Biologia Celular / Doutor em Biologia Celular e Estrutural

O principal objetivo deste trabalho é o de estabelecer uma estratégia confiável relacionada a genotoxicidade, proteção genômica e recombinação mitótica em Aspergillus nidulans. A genotoxicidade foi induzida por vapor de benzeno e, para testar a proteção genômica, a soja foi usada devido às suas propriedades anticarcinogênicas muito conhecidas. O principal resultado obtido foi que a soja transgênica mostrou maiores propriedades antigenotóxicas do que a soja tradicional. Isto foi duplamente confirmado, tanto através de estratégias de genética clássica, como molecular. Além disso, cada experimento foi repetido três vezes. Principais conclusões foram as seguintes: a) estabelecimento de um protocolo adequado para atender às complexidades dos eventos epigenéticos e, b) a aplicação desse tal protocolo e experimentos afins para testar outros agentes ambientais suspeitos de apresentarem propriedades antigenotóxicas, ou que precisem de sua identificação como tal. Evidentemente, levando-se em conta a grande preocupação relacionada aos alimentos transgênicos e aos muitos produtos de biotecnologia, que entram no mercado, o elenco de prováveis candidatos aos tipos de testes apresentados, será muito grande. Como os resultados obtidos sugerem íntima relação entre metilação de DNA eucariótico, a recombinação mitótica e outros eventos danosos às células, os eventos envolvidos serão epigeneticamente discutidos. / Main aim is to provide a reliable approach to deal with the aspects related to induced genotoxicity, genomic protection and eukaryotic mitotic recombination in Aspergillus nidulans. Genotoxicity was benzene fumes induced, and to test genomic protection soybean has been used on account of its putative anticarcinogenic properties. Main outcome is that transgenic soybean bears higher antigenotoxic properties than traditional soybean. This has been twofold confirmed through basic genetic approaches and molecular approaches, as well. In addition, each experimental approach has been three times repeated. Additional important outcomes are: a- establishment of a reliable protocol to deal with the complexities of the epigenetic events, and b- likely use of present protocol and experimental set-up to test other environmental agents of which antigenotoxic properties are either suspected, or need precise identification. Evidently, on account of present wide concern the transgenic foodstuffs, and many other biotechnological products, as well, are obvious candidates for similar approaches. Obtained results suggest close relationships among eukaryotic DNA methylation, mitotic recombination, and other cells damaging events reputedly leading to carcinogenesis.

La méthylation de l'ADN permet, via des remodelages de la chromatine et le recrutement de diverses protéines partenaires, de réguler l'expression des gènes. Des défaillances dans ces mécanismes de régulation peuvent modifier la susceptibilité individuelle face à certaines pathologies, notamment cardiovasculaires. Bien que les différents types cellulaires puissent avoir différents profils de méthylation, l'utilisation de l'ADN provenant de cellules sanguines permet de découvrir de nouveaux mécanismes physiopathologiques. Ce projet de thèse porte sur l'intérêt des analyses d'association méthylome entier comme stratégie alternative aux études d'association génome entier ("GWAS " en anglais) pour identifier de nouveaux déterminants moléculaires de biomarqueurs du risque cardiovasculaire. Pour cela, j'avais à ma disposition deux études épidémiologiques rassemblant 573 sujets pour lesquels les niveaux de méthylation de l'ADN issus du sang périphérique ont été mesurés par une puce à ADN de haute densité couvrant plus de 300 000 sites CpG.Le premier travail que j'ai réalisé a consisté en une étude du méthylome sanguin pour identifier des profils de méthylation associés à l'indice de masse corporelle. Cette étude a permis d'identifier des marques de méthylation de l'ADN au sein du gène HIF3A dont les augmentations sont associées à une augmentation de l'indice de masse corporelle (Lancet, 2014. 383(9933):1990-8). Ces résultats suggèrent en outre que des perturbations de la voie métabolique du gène HIF3A pourraient avoir un rôle important dans la réponse biologique à l'augmentation du poids. Dans un second travail (J Lipid Res, 2014. 55(7):1189-1191), j'ai montré que la variabilité inter individuelle des niveaux de méthylation sanguin du gène CPT1A était associée à la variabilité des taux lipidiques plasmatiques. Ce travail démontre qu'il est possible de détecter à partir d'échantillons sanguins des marques de méthylation de l'ADN qui pourraient être le reflet de mécanismes épigénétiques plus spécifiques de certains types cellulaires ou de certains tissus. Le gène CPT1A est par exemple principalement exprimé dans le foie.Au cours de mon travail de thèse, j'ai également étudié l'influence de la variabilité génétique sur les niveaux de méthylation de l'ADN sanguin (Am J Hum Genet, 2015. 96(4):532-42, Nat Commun, 2015. 6:6326). Cette étude a permis d'identifier près de 3 milles gènes dont les niveaux de méthylation sont associés à la présence de polymorphismes génétiques, localisés soit au sein de ces mêmes gènes (c.-à-d. effet cis) soit à une très grande distance (plus d'une mégabase voire sur un autre chromosome) (c.-à-d. effet trans). Ces résultats ouvrent de nouvelles perspectives pour mieux appréhender la régulation transcriptionnelle de diverses voies métaboliques. / DNA methylation regulates gene expression by chromatin reshaping and the recruitment of various partner proteins. Dysregulation in these regulatory mechanisms can influence the individual susceptibility to some pathologies, including cardiovascular disorders. Although different cell types can have different methylation patterns, the use of DNA from blood cells has recently been proposed as an interesting tool to discover new epigenetic related pathophysiological mechanisms. This PhD project focuses on the interests of the methylome-wide association analyses as an alternative strategy to the fashion genome-wide association studies ("GWAS ") approach to identify new molecular determinants of cardiovascular risk biomarkers. For my project, I had access to two epidemiological studies collecting together 573 subjects in which DNA methylation levels from peripheral blood cells were measured by a high density DNA microarray that covers more than 300 000 CpG sites.The first work I conducted consisted in a study of blood methylome to identify methylation profiles associated with body mass index. This study led to the identification of DNA methylation marks at the HIF3A gene whose increases are associated with an increase in body mass index (Lancet, 2014. 383(9933):1990-8). These results suggest that a disruption of the metabolic pathway HIF3A gene could have an important role in the biological response to the increase of the weight. In a second work (J Lipid Res, 2014. 55(7):1189-1191), I showed that the inter-individual variability in CPT1A methylation levels in blood were associated with variability of plasma lipid levels. This work demonstrates that it is possible to detect DNA methylation marks from blood samples that could reflect epigenetic mechanisms that occur primarily in specific cells or tissues. The CPT1A gene is for example mainly expressed in the liver.During my PhD, I also studied the influence of the genetic variability on the methylation levels from blood DNA (Am J Hum Genet, 2015. 96(4):532-42, Nat Commun, 2015. 6:6326). This work has identified nearly 3000 genes whose methylation levels are associated with the presence of genetic polymorphisms, located either within these same genes (ie cis effect) or at a very large distance (more than one megabase or to another chromosome) (ie trans effect). These results open new perspectives to better understand the transcriptional regulation of various metabolic pathways.

La caractérisation moléculaire de la réponse des plantes aux contraintes environnementales permet de mieux comprendre les bases de l’adaptation des plantes à leur milieu, et pourrait aider à l’amélioration des plantes cultivées. L’épigénome est constitué de l’ensemble des marques présentes sur la chromatine et participe à la régulation de l’expression du génome, notamment au cours du développement. Il contribue aussi à la stabilité des génomes, notamment en empêchant la transposition des éléments transposables (ET). L’épigénome varie en fonction des contraintes environnementales et une meilleure compréhension de ces variations pourrait permettre d’apporter une vision nouvelle de l’interaction entre la plante et son environnement. Cependant, l’étendue des modifications de l’épigénome, le type de séquences affectées et les mécanismes impliqués restent à déterminer. Dans ce cadre, j’ai analysé l’impact du froid sur le méthylome du maïs, une plante à génome complexe riche en ET. Dans un premier axe, j’ai analysé le méthylome d’un génotype sensible au froid, B73, par séquençage haut-débit d’ADN traité au bisulfite de sodium (BS-seq). Cette analyse comparative entre plantes « stressées » et « non stressées » a été menée (i) à l’échelle chromosomique, sans a priori sur le niveau de variation de méthylation de l’ADN et (ii) à l’échelle locale (régions différentiellements méthylées, ou « DMR ») en fixant des niveaux de variations forts (>10%). Ces deux types d’analyses ont permis de montrer que le froid déclenche une hyperméthylation à l’échelle du génome, à laquelle se superposent des hyper- et hypométhylations à l’échelle locale. Ces variations sont observées pour les trois contextes de cytosine et dans différentes régions génomiques associées aux gènes et aux ET. Ceci suggère l’activation parallèle de plusieurs mécanismes de régulation de la méthylation de l’ADN en réponse au froid. Dans un second axe, j’ai suivi ces DMR au cours du développement et dans la descendance afin d’étudier leur transmission, en lien avec leur localisation génomique et les contextes de cytosine affectés. Dans un troisième axe, j’ai étudié le lien entre variations de méthylation et sensibilité au froid en comparant la réponse du méthylome chez trois génotypes de maïs (B73, F2 et F331) présentant une réponse phénotypique contrastée pour ce caractère. / Molecular characterization of plant response to environnemental constraints allows to both better understand plant adaptation and help crop improvement. The epigenome is composed of chromatin marks and participates to the regulation of genome expression, notably through development. It is also involved in genome stability, essentially by preventing the transposition of transposable elements (TE). The epigenome can be modified by environmental cues and better understanding this variation could give new insights on the interaction between the plant and its environnement. However, the extent of this modification, targeted sequences and underlying mecanisms remain to be elucidated. In this context, I analyzed the impact of cold on the methylome of maize, a plant with a complex genome with high proportion of TEs. In a first part, I analyzed the methylome of a cold-sensitive genotype, B73, using whole genome bisulfite sequecing (BS-seq). This comparative analysis between “stressed” and “unstressed” plants was carried out (i) at the chromosome scale, without a priori definition of a DNA methylation difference and (ii) at a localized scale (Differentially Methylated regions, « DMRs ») using high minimum methylation difference rate (10%). These two types of analysis revealed that cold triggers hypermethylation at the genome scale, as well as. hyper-and-hypo-methylation at the local scale. These variations were observed in the 3 contexts of cytosine and occur in different genomic regions associated with genes and TEs. This suggests the parallel activation of different regulatory pathways in response to cold. In a second part, I focused on following-up methylation changes through development and in the progeny in conjunction with the genomic sequences and the cytosine context involved. In a third part, I studied the relationship between methylome variations and cold sensitivity by comparing the methylomes of three maize genotypes (B73, F2 and F331) with a contrasted phenotypic response to cold.

Introduction: Glycoproteins of the major histocompatibility complex (MHC) are an irreplaceable part of immune response regulation and immune homeostasis maintenance. The regulation of the expression plays an important role in adaptive immune response. Recently, DNA methylation in regulatory areas, crucial for DNA availability to transcription factors, is one of the most researched mechanisms of this type of regulation. The DNA methylation is, among others, related to the aging processes. Increased predisposition age-related immunosenescence in higher age could result from the changes in methylation status of regulatory areas of MHC class II genes. Aims: The aim of this thesis is to analyze the methylation status of regulatory areas of DQB1 gene and to compare the differences between generations and specific alleles. The differences in the levels of DQB1 gene mRNA transcription between generations and specific alleles is also compared. Methods: Both DNA and RNA were isolated from blood samples obtained from donors of three different age groups. DNA was genotypized and modified by bisulfite conversion. The regulatory areas of DQB1 genes were then amplified and subcloned into bacteria. The positive clones were selected and subjected to DNA methylation analysis. RNA was reverse transcribed into cDNA...

Les éléments transposables sont des séquences d'ADN qui ont la capacité de se déplacer dans le génome. Ils peuvent modifier l’architecture et la régulation du génome, et sont ainsi impliqués dans de nombreux désordres pathologiques, congénitaux ou acquis. L’analyse bioinformatique des éléments transposables dans les données de séquençage est la méthode de choix pour comprendre leur biologie. Mon travail de thèse a été dédié à cette question en utilisant des données réelles et simulées. Dans un premier axe, en utilisant un système cellulaire modulant le niveau de méthylation, nous avons révélé que différentes modifications chromatiniennes répressives assurent la mise sous silence des éléments transposables lorsque la méthylation de l’ADN est perdue. Dans un second axe, à l'aide d'une stratégie de mutagenèse aléatoire, nous avons découvert une nouvelle ADN méthyltransférase, spécialisée dans la méthylation des transposons jeunes au cours de la spermatogenèse. De par la nature répétée des éléments transposables, l'analyse des transposons dans les données de séquençage reste cependant un véritable défi. Finalement, dans un troisième temps, j’ai eu recours à une stratégie de simulation pour comparer les différentes méthodes d’alignement et de quantification dans les génomes murin et humain. J'ai ainsi pu élaborer des recommandations pour l'étude des éléments transposables et révéler les limites de détection de certaines familles de transposons. / Transposable elements are DNA sequences that have the ability to move in the genome. They can modify the architecture and the regulation of the genome, and be implicated in different pathological, congenital or acquired disorders. The transposon analysis with sequencing data is the first choice method to understand their biology. My thesis work was dedicated to this question using real and simulated data. In a first research axis, using a cellular system to modulate DNA methylation levels, we revealed that different repressive chromatin modifications ensure the silencing of transposable elements when DNA methylation is lost. In a second axis, using a random mutagenesis strategy, we discovered a new DNA methyltransferase, specialized in the methylation of young transposons during spermatogenesis. However, the analysis of transposons in sequencing datasets is a bioinformatic challenge because of the repeated nature of transposable elements. Eventually, in a third axis, using a simulation strategy applied to the mouse and the human genomes, I systematically compared different alignment and quantification tools. I was able to draw recommendations for the analysis of transposons and to reveal the limits in detecting specific transposons families.

Epigenetic changes represent chemical modifications of the DNA molecule and histone proteins by which gene expression is altered. Among them, DNA methylation is a known mechanism of silencing of tumor-suppressor and DNA repair genes, with an important role in carcinogenesis. Many studies have been done in order to identify the methylation signatures of these genes in different types of cancer. In our study, we investigated the methylation status of promoter regions of eight mismatch repair genes (MLH1, MSH2, MSH3, MLH3, PMS1, PMS2, MSH6 and EXO1) in 45 sporadic colorectal cancer cases and 12 head and neck cancer patients. Two out of eight genes, MLH1 and MLH3, exhibited promoter methylation. The results from both groups of patients were concordant. We summarize that the methylation profiles of MLH1 and MLH3 promoters could be potential candidates for epigenetic biomarkers in colorectal cancer, and eventually in head and neck cancer. Further investigations, which would confirm this theory, should be carried out.

De nombreuses études suggèrent que la maltraitance à l’enfance est un facteur de risque important lié à l’émergence de symptômes dépressifs à l’âge adulte. Toutefois, les mécanismes biologiques qui sous-tendent cette association demeurent méconnus. Ainsi, cette étude vise à examiner le rôle de la méthylation de l’ADN et de la réactivité au stress dans l’association entre les expériences de maltraitance à l’enfance et les symptômes dépressifs à l’âge adulte. L’échantillon est composé de 156 hommes âgés entre 18 et 35 ans. Les expériences de maltraitance et les symptômes dépressifs ont été mesurés à l’aide de questionnaires auto- rapportés. La sécrétion de cortisol, une hormone sécrétée en situation de stress, a été mesurée en réponse au Trier Social Stress Test. La méthylation de l’ADN de neufs gènes candidats (COMT, FKBP5, IL-6, IL-10, MAOA, NR3C1, OXTR, SLC6A3 et SLC6A4) a été quantifiée à l’aide du système Sequenom EpiTYPER suite à l’extraction de l’ADN salivaire. Les résultats indiquent que la méthylation de l’ADN n’explique pas l’association entre les expériences de maltraitance à l’enfance et les symptômes dépressifs à l’âge adulte et les associations sous-jacentes à l’effet indirect de la méthylation de l’ADN ne varient pas en fonction de la réactivité cortisolaire au stress. Néanmoins, les résultats de l’étude suggèrent que les expériences de maltraitance et les symptômes dépressifs sont associées à des changements dans les profils de méthylation de l’ADN. Enfin, ces résultats soulignent l’importance de réduire la prévalence de la maltraitance à l’enfance afin de limiter l’apparition de symptômes dépressifs à l’âge adulte. / Increasing evidence suggests that child maltreatment is a significant risk factor for the emergence of depressive symptoms in adulthood. However, the mechanisms underlying this association remain poorly understood. The present study examined the mediating role of DNA methylation and the moderating role of stress reactivity in the association between child maltreatment and depressive symptoms in emerging adulthood. The sample comprised 156 young male adults aged between 18 and 35 years. Maltreatment experiences and depressive symptoms were assessed using self-reported questionnaires. Cortisol, a hormone secreted in response to stress, was measured in response to the Trier Social Stress Test. DNA methylation of nine candidate genes (COMT, FKBP5, IL-6, IL-10, MAOA, NR3C1, OXTR, SLC6A3 et SLC6A4) was quantified using the Sequenom EpiTYPER technology after the extraction of salivary DNA. Results suggest that DNA methylation did not explain the association between child maltreatment and depressive symptoms in emerging adulthood, and that the associations underlying the mediating effect of DNA methylation did not vary according to the cortisol stress response. Nonetheless, the results suggest that maltreatment experiences and depressive symptoms are both associated with changes in DNA methylation profiles. Finally, these findings underscore the importance of reducing the prevalence of child maltreatment in order to limit the onset of depressive symptoms in emerging adulthood.

In the mammalian genome, 5‟-CpG-3‟ dinucleotides are frequently methylated, correlating with transcriptional silencing. Genome-wide waves of demethylation are thought to occur only twice during development, in primordial germ cells and in the pre-implantation embryo. They are followed by de novo methylation, setting up a pattern that is inherited throughout development. No global methylation changes are thought to occur during further somatic development, although methylation does alter at gene-specific loci, contributing to tissue-specific patterns of gene expression. Here we studied DNA methylation in differentiating mouse erythroblasts in vivo using several approaches including genomic-scale, reduced representation bisulfite sequencing (RRBS). Surprisingly, demethylation at the erythroid-specific β-globin locus was coincident with a wave of global DNA demethylation at most genomic elements, including repetitive elements and genes silenced in erythropoiesis. Over 30% of total methylation is irreversibly lost during erythroid differentiation. Demethylation occurred through a passive mechanism, requiring the rapid DNA replication triggered with the onset of erythroid terminal differentiation. Global loss of DNA methylation was not associated with a global increase in transcription, as determined by GeneChip analysis. We propose that global demethylation is a consequence of cellular mechanisms required for the rapid demethylation and induction of β-globin and other erythroid genes. Our findings demonstrate that, contrary to previously held dogma, DNA demethylation can occur globally during somatic cell differentiation, providing a new experimental model for the study of global demethylation in development and disease.

Contexte et objectif : Plusieurs facteurs de risque de cancer ont été identifiés et il a été estimé que plus de 40% des cas dans les pays développés pourraient être évités en modifiant les facteurs de risque connus. L'objectif général de cette thèse était de démontrer que l’intégration de données génomiques et épigénomiques aux données détaillées sur les expositions environnementales et le mode de vie peut être utile pour identifier des biomarqueurs de ces facteurs et contribuer à augmenter notre connaissance de l'étiologie du cancer. Résultats : Dans un premier temps, nous décrivons comment les signatures génomiques et épigénomiques peuvent être utilisées pour identifier des marqueurs d’exposition et déchiffrer l’étiologie du cancer. Ensuite, nous contribuons au débat relatif à l’hypothèse de la chance dans le développement du cancer et démontrons que les mutations induites par le tabagisme sont plus prédictives du risque de cancer que les mutations aléatoires. Nous introduisons un modèle probabiliste pour la simulation de données mutationnelles et comparons la performance des outils d’identification de ces signatures avec des données réelles et simulées. De plus, nous introduisons une nouvelle méthode pour l’identification des signatures mutationnelles. Enfin, nous utilisons les données de méthylation de la cohorte E3N pour étudier le lien entre l'exposition aux retardateurs de flamme bromés et aux composés perfluorés, deux substances classées parmi les perturbateurs endocriniens, et la méthylation de l’ADN sanguin. Globalement, notre étude ne fournit aucune preuve d'altérations globales du méthylome ou d'altérations à l’échelle des CpGs. Cependant, certains résultats suggèrent l’existence d'altérations de la méthylation de gènes impliqués dans des voies biologiques (ex., la réponse aux androgènes) et nécessitent des recherches supplémentaires.Conclusion : Ce travail contribue à la recherche méthodologique portant sur les signatures mutationnelles en introduisant un protocole de mesure de performance et d’identification des signatures mutationnelles pouvant servir de référence à de futures études méthodologiques ou appliquées. Nos recherches sur les signatures mutationnelles et le méthylome démontrent l'utilité de tels outils pour évaluer les expositions et élucider leur rôle dans l'étiologie du cancer. / Context and aim: Several risks factors have been identified for cancer, and it has been estimated that more than 40% of cases in developed countries are preventable through the modulation of known modifiable risk factors. The overall objective of this thesis was to demonstrate that the analysis of genomic and epigenomic data integrated with well-characterised exposure and lifestyle data may be used to identify markers of environmental exposures and lifestyle and may contribute to increase our understanding of cancer aetiology.Results: We first describe how genomic and epigenomic signatures can be used to identify markers of exposure and decipher the aetiology of cancer. Then, we adopt the mutational signatures framework to contribute to the debate about the “bad luck” hypothesis for cancer and demonstrate that tobacco-related mutations are more strongly correlated with cancer risk than random mutations. We introduce a probabilistic model for the simulation of mutational signature data and compare the performance of the available methods for the identification of mutational signatures using both simulated and real data. Additionally, we introduce a new method for the identification of such signatures. Finally, we use methylation array data in an epidemiological study within the E3N cohort to investigate the association between exposure to Brominated Flame Retardants and Per- and polyfluoroalkyl substances, two organic pollutants that are known endocrine disrupting chemicals, and methylation in DNA from blood. Overall, our study does not provide evidence of methylation alterations at the level of the whole genome, in regions or in single CpGs. Suggestive evidence of alterations in the methylation of genes within plausible biological pathways (e.g. androgen response) warrants further investigations. Conclusion: Our work on the methodological aspects of mutational signature research introduces an original framework for measuring the performance of tools for the identification of mutational signatures that may serve as reference for future methodological or applied research. Our applications of both mutational signature and methylome research demonstrate the usefulness of such tools to assess exposures and elucidate their role in cancer aetiology.